It appears that with 5.1.0f3 Physics2D.BoxCasts will not detect a collider if it starts inside of it. I ran a simple scene test where a Physics2D.BoxCast is cast across the collider and this works fine, but if the BoxCast starts in the collider then it won’t detect it.
Yes the option ‘Raycasts Start in Colliders’ is checked in the Physics 2D settings.
Worth noting that Physics2D.RayCast does not appear to have this issue.